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Re: fem-fenics 0.0.1 released


From: Marco Vassallo
Subject: Re: fem-fenics 0.0.1 released
Date: Mon, 24 Feb 2014 15:13:08 +0000




On Mon, Feb 24, 2014 at 3:04 PM, <address@hidden> wrote:
On Sunday, February 23, 2014 08:36 PM, Juan Pablo Carbajal wrote:
On Sun, Feb 23, 2014 at 9:18 AM, Marco Vassallo <address@hidden> wrote:
The solutions seems to be to set the CPPFLAGS as follow

export CPPFLAGS="-I/usr/include/eigen3 $(mpicxx -showme:compile)"

Indeed this should solve the problem,
just find where "Dense" is installed. Try
  locate Eigen/Dense
in your terminal, you should add that path to CPPFLAGS as Marco explained.

To see if mpi is properly installed you can run
  mpicxx -showme:compile
in your terminal as well. If you get an error, then you need to install openmpi.


Thanks! It solved the dolfin.h not found problem. I also found out that setting CPPFLAGS to -I/usr/include/eigen3 alone is sufficient. In order to use the package, it has to be set before starting octave as well. Otherwise I still get "Eigen/Dense not found" when fem-fenics is run.

One more glitch is, for example, when trying the one of the femfenics_examples, octave exits and threw this error:

symbol lookup error: /usr/lib/openmpi/lib/openmpi /mca_paffinity_linux.so: undefined symbol: mca_base_param_reg_int

I searched a bit and found that it seems to be specific to openmpi only and quite common when openmpi is called from scripting languages. It's related to how openmpi loads its supporting libraries.

http://www.open-mpi.org/faq/?category=running#loading-libmpi-dynamically

Unfortunately I'm not much of a developer to meddle in the code to implement the recommendation, though. :-(

 
I had exactly the same issue using Ubuntu, but with Mac OS X it doesn't seems to be a problem.
However I don't know exactly how to solve it because in the code I've written
I never call directly mpi; probably it is used from dolfin somewhere else but I can't figure out how to fix it.
If anyone has any suggestion...

Marco
A workaround is to preload it with something like

export LD_PRELOAD=/usr/lib/openmpi/lib/libmpi.so

before starting octave.

Thanks again for making fenics available in octave. It's great now octave can interface with a full blown FEM code,

Regards,
ST
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